Package: sdtm.oak 0.2.0

Rammprasad Ganapathy

sdtm.oak: SDTM Data Transformation Engine

An Electronic Data Capture system (EDC) and Data Standard agnostic solution that enables the pharmaceutical programming community to develop Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM) datasets in R. The reusable algorithms concept in 'sdtm.oak' provides a framework for modular programming and can potentially automate the conversion of raw clinical data to SDTM through standardized SDTM specifications. SDTM is one of the required standards for data submission to the Food and Drug Administration (FDA) in the United States and Pharmaceuticals and Medical Devices Agency (PMDA) in Japan. SDTM standards are implemented following the SDTM Implementation Guide as defined by CDISC <https://www.cdisc.org/standards/foundational/sdtmig>.

Authors:Rammprasad Ganapathy [aut, cre], Adam Forys [aut], Edgar Manukyan [aut], Rosemary Li [aut], Preetesh Parikh [aut], Lisa Houterloot [aut], Yogesh Gupta [aut], Omar Garcia [aut], Ramiro Magno [aut], Kamil Sijko [aut], Shiyu Chen [aut], Pattern Institute [cph, fnd], F. Hoffmann-La Roche AG [cph, fnd], Pfizer Inc [cph, fnd], Mohsin Uzzama [aut], Transition Technologies Science [cph, fnd]

sdtm.oak_0.2.0.tar.gz
sdtm.oak_0.2.0.zip(r-4.7-any)sdtm.oak_0.2.0.zip(r-4.6-any)sdtm.oak_0.2.0.zip(r-4.5-any)
sdtm.oak_0.2.0.tgz(r-4.6-any)sdtm.oak_0.2.0.tgz(r-4.5-any)
sdtm.oak_0.2.0.tar.gz(r-4.7-any)sdtm.oak_0.2.0.tar.gz(r-4.6-any)
sdtm.oak_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sdtm.oak/json (API)

# Install 'sdtm.oak' in R:
install.packages('sdtm.oak', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pharmaverse/sdtm.oak/issues

Pkgdown/docs site:https://pharmaverse.github.io

Datasets:

On CRAN:

Conda:

8.58 score 79 stars 159 scripts 699 downloads 25 exports 43 dependencies

Last updated from:6b5d887aa5. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK136
source / vignettesOK289
linux-releaseOK166
macos-releaseOK134
macos-oldrelOK113
windows-develOK100
windows-releaseOK105
windows-oldrelOK103
wasm-releaseOK128

Exports:%.>%assign_ctassign_datetimeassign_no_ctcal_min_max_datecondition_addcreate_iso8601ct_mapct_spec_examplederive_blflderive_seqderive_study_daydomain_examplefmt_cmpgenerate_oak_id_varsgenerate_sdtm_supphardcode_cthardcode_no_ctoak_cal_ref_datesoak_id_varsproblemsread_ct_specread_ct_spec_exampleread_domain_examplesbj_vars

Dependencies:admiraldevassertthatbrewcallrclicommonmarkcpp11descdplyrevaluatefsgenericsgluehighrknitrlifecyclelubridatemagrittrotelpillarpkgbuildpkgconfigpkgloadprocessxpspurrrR6rdtoolsrlangroxygen2rprojrootstringistringrtibbletidyrtidyselecttimechangeutf8vctrswithrxfunxml2yaml

Creating an Findings SDTM domain
Introduction | Programming workflow | Read in data | Create oak_id_vars | Read in CT | Map Topic Variable | Map Rest of the Variables | Repeat Map Topic and Map Rest | Create SDTM derived variables | Add Labels and Attributes
Rendered fromfindings_domain.Rmdusingknitr::rmarkdown

Last update: 2024-11-12
Started: 2024-07-30

Creating an Interventions SDTM domain
Introduction | Raw data | Programming workflow | Read in data | Create oak_id_vars | Read in CT | Map Topic Variable | Map Rest of the Variables | assign_no_ct | assign_ct | assign_datetime | hardcode_ct and condition_add | hardcode_no_ct and condition_add | condition_add involving target domain | condition_add involving raw dataset and target domain | Repeat Map Topic and Map Rest | Create SDTM derived variables | Add Labels and Attributes
Rendered frominterventions_domain.Rmdusingknitr::rmarkdown

Last update: 2024-11-12
Started: 2024-11-12

Path to Automation
Standards Metadata | Study Definition Metadata | Study SDTM Mappings Metadata (specifications)
Rendered fromstudy_sdtm_spec.Rmdusingknitr::rmarkdown

Last update: 2024-07-31
Started: 2024-07-30

Algorithms & Sub-Algorithms
Core Concept | List of Algorithms | Sub-algorithms
Rendered fromalgorithms.Rmdusingknitr::rmarkdown

Last update: 2024-07-30
Started: 2024-07-30

Conditioned Data Frames
Introduction | Creating Conditioned Data Frames | Simple Example | Usage in SDTM Domain Derivations | Example with Concomitant Medications (CM) Domain
Rendered fromcnd_df.Rmdusingknitr::rmarkdown

Last update: 2024-07-30
Started: 2024-07-30

Converting dates, times or date-times to ISO 8601
Introduction | Multiple inputs | Format variations | Multiple alternative formats | Parsing of date or time components | Allowing alternative date or time values | Changing reserved format characters
Rendered fromiso_8601.Rmdusingknitr::rmarkdown

Last update: 2024-07-30
Started: 2024-07-30

Readme and manuals

Help Manual

Help pageTopics
Explicit Dot Pipe%.>%
Derive an ISO8601 date-time variableassign_datetime
Derive an SDTM variableassign assign_ct assign_no_ct
Calculate minimum and maximum date and time in the data framecal_min_max_date
Add filtering tags to a data setcondition_add
Convert date or time collected values to ISO 8601create_iso8601
Recode according to controlled terminologyct_map
Find the path to an example controlled terminology filect_spec_example
Conditioned tibble pillar print methodctl_new_rowid_pillar.cnd_df
Derive Baseline Flag or Last Observation Before Exposure Flagderive_blfl
Derive the sequence number ('--SEQ') variablederive_seq
'derive_study_day' performs study day calculationderive_study_day
Find the path to an example SDTM domain filedomain_example
Date/time collection formatsdtc_formats
Regexps for date/time format componentsfmt_cmp
A function to generate oak_id_varsgenerate_oak_id_vars
Function to generate final SDTM domain and supplemental domain SUPP-generate_sdtm_supp
Derive an SDTM variable with a hardcoded valueharcode hardcode_ct hardcode_no_ct
Mutate method for conditioned data framesmutate.cnd_df
Calculate Reference dates in ISO8601 character format.oak_cal_ref_dates
Raw dataset keysoak_id_vars
Retrieve date/time parsing problemsproblems
Read in a controlled terminologyread_ct_spec
Read an example controlled terminology specificationread_ct_spec_example
Read an example SDTM domainread_domain_example
Subject-level key variablessbj_vars
Conditioned tibble header print methodtbl_sum.cnd_df